The hPDB package


Protein Data Bank file format is a most popular format for holding biological macromolecular data.

This is a very fast sequential parser:

In its parallel incarnation it is most probably the fastest parser for PDB format.

It is aimed to not only deliver event-based interface, but also a high-level data structure for manipulating data in spirit of BioPython's PDB parser.

hPDB - Haskell library for processing atomic biomolecular structures in Protein Data Bank format - Michal Jan Gajda. BMC Research Notes 2013, 6:483.


Versions0.99, 0.999, 0.9999, 0.9999.1, 1.0, 1.1, 1.1, 1.1.1, 1.1.2, 1.2.0,,,,
DependenciesAC-Vector, base, bytestring, containers, deepseq, directory, ghc-prim, iterable (>=2.0), mmap, mtl, Octree (>=0.5), parallel (>=, QuickCheck (>=, template-haskell, text (>=, text-format (>=, vector, zlib
CopyrightCopyright by Michal J. Gajda '2009-'2013
AuthorMichal J. Gajda
Home page
Source repositoryhead: git clone
head: git clone git://
UploadedSun Dec 8 19:07:01 UTC 2013 by MichalGajda



have-mmapUse mmap to read input faster.Enabled
have-sse2Use -msse2 for faster code.Enabled
have-text-formatDo not use text-format, since it may require double-conversion and thus linking of libstdc++ which may break compilation due to GHC bug #5289:
old-bytestringUse bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6.Disabled
old-zlibUse zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1Disabled
old-vectorUse old vector library before version 0.10 (introduced along with GHC 7.6). Disable for GHC 7.6.1 and latest 7.4.2.Disabled

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